HorA Server Transitive Detail

Reference:
H. Cheng, BH. Kim, and N. Grishin (2008). Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable datasets. J. Mol. Biol. 377(4): 1265-1278
BH. Kim, H. Cheng, and N. Grishin (2009). HorA web server to infer homology between proteins using sequence and structural similarity. Nucleic Acids Res. 37(Web Server issue):W532-8
Comments and suggestions to: grishin@chop.swmed.edu


Query: T542_A.pdb A
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 1.669 --> Intermediate <-- 1.293 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1f8fa2) through the intermediate protein (d1vl2a1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1vl2a1 Argininosuccinate synthetase,​ N-​terminal domainAdenine nucleotide alpha hydrolases-​likeAdenine nucleotide alpha hydrolase-​likeα/β
Hit d1f8fa2 Benzyl alcohol dehydrogenaseNAD(P)-​binding Rossmann-​fold domainsNAD(P)-​binding Rossmann-​fold domainsα/β

Supporting Alignments

Query <-- 1.669 --> Intermediate
DALI alignment (Z-score: 12.4 Raw score:948.50) query 1 slqlrlalnqidstvgdiagnaeailrwtrhsaeqgahlvafpemaltgypvedlalrss 60 d1vl2a1 1 ------------------------------------------------------------ 1 query 61 fveasrtalrelaarlaeegfgelpvlvgyldrsesaqpkygqpagaprnaaavlhrgrv 120 d1vl2a1 1 ------------------------------------------------------------ 1 query 121 altfakhhlpnygvfdefryfvpgdtmpivrlhgvdialaicedlwqdggrvpaarsaga 180 d1vl2a1 1 ------------------------------------------------------------ 1 query 181 glllsvnaspyerdkddtrlelvrkraqeagcttaylamiggqdelvfdgdsivvdrdge 240 d1vl2a1 1 ------------------------------------------------------------ 1 query 241 vvarapqfsegcvvldldlpaaeaepptgvvddglridrlviseeplpayeaelaggyad 300 d1vl2a1 1 ------------------------------------------------------------ 1 query 301 rldadeevysalvvglrayvakngFRSVLIGLSGGIDSALVAAIACDALGaqNVYGVSMP 360 :::::::::::::::::::::::::: :::::::: d1vl2a1 1 ------------------------KEKVVLAYSGGLDTSVILKWLCEKGF--DVIAYVAN 34 query 361 SKySSDHsKGDAAELARRTGL-NFRTVSIEPMFDAY-MASLG-------ltGLAEENLQS 411 :: :::: ::::::::::::: :::::::::::::: ::::: ::::::::: d1vl2a1 35 VG-QKDD-FVAIKEKALKTGAsKVYVEDLRREFVTDyIFTALlgnamyegrYLLGTAIAR 92 query 412 RLRGTTLMAISNQEGH-IVLAPGNKselavGYST-lyGDSV--------gAYGPIK---- 457 :::::::::::::::: :::::::: :::: :::: :::::: d1vl2a1 93 PLIAKRQVEIAEKEGAqYVAHGATG-----KGNDqvrFELTyaalnpnlkVISPWKdpef 147 query 458 DVYK-TSIFRLAEWRnraaaergqtPPIPeasitkpdypvldailelyvdrdtgadaiva 516 :::: :::::::::: :::: d1vl2a1 148 LAKFkTDLINYAMEK----------GIPI------------------------------- 166 query 517 agydrelvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnrwregh 568 d1vl2a1 167 ---------------------------------------------------- 167 FAST alignment (Normalized score: 5.35 Raw score:1644.00) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1vl2a1 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1vl2a1 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1vl2a1 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1vl2a1 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1vl2a1 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGF-RSVLIGLSGGIDSALVAAIACDALGAQNVYGVSM 359 :::::::::::::::::::::: ::: ::::::: d1vl2a1 1 -------------------------KEKVVLAYSGGLDTSVILKWLCE-KGF-DVIAYVA 33 query 360 PS-KYS-SDHSKGDAAELARRTG---LNFRTVSIEPMFD-AYMA---SLGLTGL------ 404 :: ::: :::::::::: ::::::::::::: :::: :::: d1vl2a1 34 NVGQKDDFVAIKEKALK------TGASKVYVEDLRREFVTDYIFTALLGNA---MYEGRY 84 query 405 -AEENLQSRLRGTTLMAISNQEG-HIVLAPGNKSELAVGYSTLY------GDSVG----- 451 :::::::::::::::::::::: :::::::::: :::: d1vl2a1 85 LLGTAIARPLIAKRQVEIAEKEGAQYVAHGATGK----------GNDQVRFELT-YAALN 133 query 452 ----AYGPIKDVY----------KTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVL 497 :::: :::::::::: d1vl2a1 134 PNLKVISP-----WKDPEFLAKFKTDLINYAME--------------------------- 161 query 498 DAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRR 557 d1vl2a1 162 ------------------------------------------------------------ 162 query 558 LPITNRWREGH----- 568 d1vl2a1 162 -----------KGIPI 166 TMalign alignment (TM-score: 0.23 Raw score:131.95) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1vl2a1 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1vl2a1 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1vl2a1 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1vl2a1 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1vl2a1 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMP 360 :::::::::::::::::::::::::: :::::::: d1vl2a1 1 ------------------------KEKVVLAYSGGLDTSVILKWLCEKGF--DVIAYVAN 34 query 361 SKYSSDHSKGDAAELARRTGL-NFRTVSIEPMFDAY-MASLG---LT----GLAEENLQS 411 :: :::: ::::::::::::: :::::::::::::: ::::: :: ::::::::: d1vl2a1 35 VG-QKDD-FVAIKEKALKTGASKVYVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIAR 92 query 412 RLRGTTLMAISNQEGH-IVLAPGNKSELAVGYSTLYGDS-VG--------AYGPIK-D-- 458 :::::::::::::::: :::::::: : :::::::: :: :::::: : d1vl2a1 93 PLIAKRQVEIAEKEGAQYVAHGATG--K---GNDQVRFELTYAALNPNLKVISPWKDPEF 147 query 459 VYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAG 518 :: :::::::::::: : : ::: d1vl2a1 148 LA-KFKTDLINYAME-K------G-IPI-------------------------------- 166 query 519 YDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 568 d1vl2a1 167 -------------------------------------------------- 167 HHsearch alignment (Probability: 0.96 E-value:0.00) query 326 RSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGL-NFR 384 ::::::::::::::::::::::: :::::::::: ::::::::::::::::::: ::: d1vl2a1 2 EKVVLAYSGGLDTSVILKWLCEK--GFDVIAYVAN--VGQKDDFVAIKEKALKTGASKVY 57 query 385 TVSIEPMFDAYM--------ASLGLTGLAEENLQSRLRGTTLMAISNQEGHIVLAPG--- 433 :::::::::::: ::::::::::::::::::::::::::::::::::::: d1vl2a1 58 VEDLRREFVTDYIFTALLGNAMYEGRYLLGTAIARPLIAKRQVEIAEKEGAQYVAHGATG 117 query 434 ---NKSELAVGYSTLYGDSVGAYGP-----IKDVYKTSIFRLAEWRN 472 ::::::::::::::: :::::: ::::::::::::::::: d1vl2a1 118 KGNDQVRFELTYAALNPN-LKVISPWKDPEFLAKFKTDLINYAMEKG 163
Intermediate <-- 1.293 --> Hit
DALI alignment (Z-score: 6.0 Raw score:520.70) d1vl2a1 1 ----------------------------KEKVVLAYSGGlDTSVILKWLCEKGF-DVIAY 31 ::::::::::: :::::::::::::: ::::: d1f8fa2 1 vpiellgplgcgiqtgagacinalkvtpASSFVTWGAGA-VGLSALLAAKVCGAsIIIAV 59 d1vl2a1 32 VAnvgqkddFVAIKEKALKTGASKVYVEDLrrefvtdyiftallgnamyegryllgtaia 91 :: ::::::::::::::::::::: d1f8fa2 60 DI-------VESRLELAKQLGATHVINSKT------------------------------ 82 d1vl2a1 92 rpliakRQVEIAEKEG---AQYVAHGAtgkgnDQVRFELTYA-alNPNLKVIS------- 140 :::::::::: :::::::: :::::::::: :::::::: d1f8fa2 83 -----qDPVAAIKEITdggVNFALEST-----GSPEILKQGVdalGILGKIAVvgapqlg 132 d1vl2a1 141 ----------------pwKDPEFLA---kFKTDLINYAMEkgipi 166 ::::::: ::::::::::: d1f8fa2 133 ttaqfdvndlllggktilGVVEGSGspkkFIPELVRLYQQ---gk 174 FAST alignment (Normalized score: 5.93 Raw score:1007.00) d1vl2a1 1 ----------------------------KEKVVLAYSGGLDTSVILKWLCEKGF-DVIAY 31 :::::: ::::::::::::::::::: ::::: d1f8fa2 1 VPIELLGPLGCGIQTGAGACINALKVTPASSFVT-WGAGAVGLSALLAAKVCGASIIIAV 59 d1vl2a1 32 VANVGQKDD-FVAIKEKALKTGASKVYVEDLRREFVTDYIFTALLGNAMYEGRYLLGTAI 90 : ::::::::::::::::::: d1f8fa2 60 D--------IVESRLELAKQLGATHVINS------------------------------- 80 d1vl2a1 91 ARP---LIAKRQVEIAEKE---GAQYVAHGATG--KGNDQVRFELTYAAL-NPNLKVISP 141 ::::::::: :::::::: ::::::::::: ::::::::: d1f8fa2 81 ---KTQDPVAAIKEI----TDGGVNFALES---TGSPEILKQGVDA----LGILGKIAVV 126 d1vl2a1 142 WKDPEFLAKF------------------------------------KTDLINYAMEKGIP 165 ::::::::: d1f8fa2 127 ----------GAPQLGTTAQFDVNDLLLGGKTILGVVEGSGSPKKFIPELVRLYQ----- 171 d1vl2a1 166 I--- 166 d1f8fa2 172 -QGK 174 TMalign alignment (TM-score: 0.45 Raw score:74.82) d1vl2a1 1 -----------KEKVVLAYSGGL-DTSVILKW-LCEKGFD--VIAYVANVGQKD-DFVAI 44 :: :::::::: :: :: ::::::: ::: : :: d1f8fa2 1 VPIELLGPLGC----------GIQTGAGACINALK---VTPASSFVTWG--AGAV-G-LS 43 d1vl2a1 45 KEKALKTGAS-KVYV-------------------EDLRREF------------------- 65 :::::::::: :::: ::::::: d1f8fa2 44 ALLAAKVCGASIIIAVDIVESRLELAKQLGATHVINSKTQDPVAAIKEITDGGVNFALES 103 d1vl2a1 66 VTDYIFTALLGNAMYEGRYLLGTAIARPLIAKRQVEIAEKEGAQYVAHGATGKGNDQVRF 125 :: :::::::::::: :::::::::: :::::: d1f8fa2 104 ----------------------TG--SPEILKQGVDAL--GILGKIAVVG---APQLGT- 133 d1vl2a1 126 ELTYAALN--PN---LKVISPWKDPEFLAKFKTDLINYAMEKGI--PI 166 ::: ::: :: ::::::::: :: :: ::::::::: :: :: d1f8fa2 134 TAQ--FDVNDLLLGGKTILGVVEG--SG-SP-KKFIPELVR-LYQQGK 174 HHsearch alignment (Probability: 0.04 E-value:0.12) d1vl2a1 2 EKVVLAYSGGLDTSVILKWLCEKGF-DVIAYVANVGQKDDFVAIKEKALKTGASKVYVED 60 ::::::::::::::: ::::::::: ::::::: :::::::::::::::: :: d1f8fa2 30 SSFVTWGAGAVGLSA-LLAAKVCGASIIIAVDI-------VESRLELAKQLGATHV--IN 79 d1vl2a1 61 LRREFVTDYIFTALLGNAMYEGRYLLGTAIARPLIAKRQVEIAEKEGAQYVAHGATGKGN 120 ::::::::::::::: ::::::::::::::::::::::::::: ::::::::: :: d1f8fa2 80 SKTQDPVAAIKEITD-----GGVNFALESTGSPEILKQGVDALGILG-KIAVVGAPQ-LG 132 d1vl2a1 121 DQVRFELTYAALNPNLKVIS 140 ::::::: :::::::::::: d1f8fa2 133 TTAQFDV-NDLLLGGKTILG 151